Contacts of the strand formed by residues 296 - 299 (chain F) in PDB entry 6IWQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 296 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207F LEU* 3.6 28.7 - - + -
208F THR 3.1 12.6 + - - +
209F SER* 3.2 17.4 - - - +
210F SER 2.9 25.5 + - - +
294F GLY 4.3 1.1 - - - -
295F GLN* 1.3 82.5 + - - +
297F LEU* 1.3 78.3 + - - +
298F ILE* 3.9 8.1 - - + -
315F VAL* 4.1 11.9 - - + -
318F ILE* 4.3 19.7 - - + -
393F ALA* 4.5 0.9 - - + -
394F ILE 3.4 13.0 - - - +
395F GLU* 3.9 4.9 - - - +
396F ARG 3.8 0.2 - - - +
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Residues in contact with LEU 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F SER* 3.6 19.7 - - - +
212F VAL* 4.4 12.6 - - + -
288F ALA* 3.6 31.6 - - + -
291F ALA* 4.4 6.3 - - + +
294F GLY 5.7 0.2 - - - +
296F VAL* 1.3 78.1 - - - +
298F ILE* 1.3 61.0 + - - +
299F TYR* 3.7 24.9 - - + +
392F PHE 3.7 1.0 - - - +
393F ALA* 3.1 6.4 - - - -
394F ILE* 2.7 35.1 + - + +
396F ARG* 3.9 39.3 - - + +
399F PHE* 4.1 14.1 - - + -
400F PHE* 5.2 0.4 - - + -
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Residues in contact with ILE 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209F SER* 3.4 29.8 - - - +
210F SER 2.9 7.5 + - - -
211F VAL* 3.1 18.3 - - + +
212F VAL* 2.9 23.6 + - - -
296F VAL* 3.9 5.8 - - + -
297F LEU* 1.3 77.8 - - - +
299F TYR* 1.3 63.3 + - - +
300F LEU* 4.3 15.0 - - + -
310F TRP* 3.6 32.3 - - + -
311F TYR* 3.5 27.4 - - + -
314F LEU* 4.0 19.3 - - + -
315F VAL* 4.2 2.0 - - + -
392F PHE 3.5 5.2 - - - +
393F ALA* 4.2 2.7 - - + -
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Residues in contact with TYR 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F VAL* 3.1 31.9 - - + -
214F VAL* 5.4 1.1 - - + -
284F ARG* 3.0 57.0 + - + +
288F ALA* 3.2 22.3 - - - +
297F LEU* 3.7 26.0 - - + -
298F ILE* 1.3 77.8 - - - +
300F LEU* 1.4 70.3 - - - +
390F GLY 4.3 6.7 - - - +
391F LEU* 3.2 17.1 - - - -
392F PHE* 2.8 54.3 + + + +
394F ILE* 5.3 0.2 - - + -
399F PHE* 3.4 17.1 - + - -
405F TYR* 5.8 0.2 - + - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il